My answer is that they are an important part of
Star Trek's consistency. Other figures such as warp speed or
phaser power often lead to pointless discussions because they are quite abstract.
In contrast, a physical dimension is
something much more definite because it can be determined without any knowledge
about fictitious subspace physics or the rapid nadion effect. We just need to remembers
that starships are built to accommodate humans or humanoids to recognize that
size does matter.

General Considerations

In spite of everything, starship sizes are often
unknown or, even worse, in dispute. The reason is that they are
no real-world objects designed for and built in a certain size. There is a model (hardware or CGI) of each
ship. The
size of the "real" ship, however, depends not only on what the model looks
like but also on how it is presented on screen. Kitbashed designs and scaling
up and down an existing design
often obstruct the size estimation. Basically, there are three
possible references to determine the size of a starship:

Outer/inner structure The decks of Federation starships are usually around
3.5m tall, confirmed by the interior sets whose basic dimensions
are the same for all Federation ships and by MSDs and deck
measurements of those ships whose size and deck count
is known. The clear height of rooms and corridors on a ship is some 2.5m,
bearing in mind that 24th century humans are evidently not taller than in the
21st century. Still, civilian ships or warships may have decks of only 3m and, on the other hand,
Rick Sternbach designed the Intrepid
class with exceptionally tall decks of 4m on average (just like the Nova class
too). So unless we know how tall the decks (possibly including Jefferies
tubes between the decks) are intended to be, there is an
unacceptable uncertainty range of some 25%. Moreover, this method
doesn't work for alien vessels that often don't have window rows to
count, let alone cross-sections to shed light on their internal structure. Even if it were possible to count
the decks, the deck height is not necessarily the same as on Federation ships.

Starship encounters Starship encounters or space battles are
commonly used references, provided that trustworthy figures for at least one of the participating ships
are known. However, when analyzing the visual effects of the pre-CGI age, the
limitations of motion control photography have to be taken into account.
Occasionally two ships of different scales were filmed in one take (like the
Excelsior and Enterprise-D), moreover
naturally at a much too close distance. Shuttles sometimes can't be made as
small as they should be because they would be barely recognizable. But even in
cases where it would be technically possible to get the relative scaling right
and with modern CGI, VFX people sometimes don't do their job carefully enough or
even increase or decrease ships intentionally for the dramatic impact. So
the comparison method may yield contradictory results. A considerable error has to be taken into
account, and often the only reliable statement is something like
"the unknown ship X is bigger than ship A", or "ship X is at most
or at least y meters long".

Official/VFX sizes Size figures in official publications or given by
individuals involved in the production process (Probert, Okuda,
Sternbach, Drexler, Eaves, Stipes) are possible references likewise. However,
they should be treated judiciously, for they don't necessarily
reflect the "actual" sizes of the ships. For instance,
if the designer says his ship is x meters long, but the VFX
people evidently always assume y meters, the whole thing has to be
reconsidered. Moreover, ship sizes may be based on a preliminary sketch rather
than the final ship, or they use a faulty reference, which is the case in the Deep
Space Nine Technical Manual where, among other ships, the
well-known Excelsior is scaled up by 10%. The sizes mentioned in
several official publications are evaluated on a separate page.

A Classification System

Concerning the reliability of size figures
and of the designs themselves, I have found the following categories
of ships (however, I don't refer to them elsewhere at EAS because they are too
abstract):

Type AA
ship which has been designed in a process close to real
engineering and is well-documented, implying that the designer
has adhered to a certain size and deck count and the people in charge of the VFX
abide by this size. There is at least a
sketch of the interior layout in the form of an MSD or a similar cross-section, and it
has to match the outer appearance as indicated by window rows and
lifeboats. If such a ship is present in a scene with
contradictory size ratios, it has to be used as a reference,
rather than being scaled up or down itself. Such a design is what
it should be, a scale model, i.e. with a fixed scale and a definite size. Only the
major ships featured in the shows, the Constitution refit, Galaxy,
Intrepid and NX classes are of this type, but rather not the Defiant
and definitely not the "Star Trek
(2009)" Enterprise.

Type BA
ship which has not been designed quite as carefully as type A,
but whose size can be exactly determined due to very reliable
references. For instance, the ship employs the same components as
another ship, or there is a size chart which has been used for
both the design and the VFX. If this applies, the figures are as
reliable as those of type A. The Ambassador, Excelsior, Miranda, Constellation,
Sydney, Nebula, Prometheus, D7 and K't'inga are members of type B.

Type CA
ship whose size is not quite as evident, but can be determined
with a small uncertainty range. This is the case if the size based on the deck
count, the size comparison with other ships, a possible figure provided by the
designer
and references from literature are close together.
The error should be less than 10%. This type includes
the Akira, Oberth, D'deridex, Vor'cha,
Galor and the Ferengi Marauder.

Type DA
ship whose size stays about the same in VFX shots, but a reliable
figure is not available. Such a ship usually doesn't have window
rows to count, and it seems it has been intentionally designed
without a explicit size in mind. There are many alien ship types
in this category, for instance the Romulan
scout, Jem'Hadar "bug" and battlecruiser, (Bajoran) Antares-class
freighter and Bajoran raider, as well as the Norway, Steamrunner and Saber.

Type EA
ship whose perceived size is subject to vary and is in dispute, irrespective of
the figures given in publications, by the designer or by the VFX staff. This is the
case if a design changes its size (Defiant, Deep Space 9, "Star Trek
(2009)" Enterprise)
or if the same model is used to represent ships of intentionally different sizes
(Klingon Bird-of-Prey, Kazon
raider/fighter, Jem'Hadar battleship), both of which is
impossible. The same applies for kitbashed designs combining
scaled components such as the Yeager class.

Type FA
ship whose size is not that relevant. These are alien-of-the-week
ships for which the same model (the triangular guest starship
from TNG, for instance) is used again and again. Other ships
whose size doesn't matter that much are those which can be
described as "just huge" (Borg cube, Kazon mothership)
or "just tiny" (ships which are described as shuttles
or single-seated).

Summarizing, there are reliable figures for
type A and B ships. The sizes of type C ships are not exactly
known, but the evidence is sufficient for a good estimation.
Ships of type D are satisfactory in that there are no blatant
inconsistencies, but fans have derived different
figures all of which could be true. Essentially the same applies to the
type F ships.

This leaves the type E ships as the ones that cause the
tough problems because of the contradictory evidence. There is no
solution but to find a suited compromise, or to take the average
of the shown VFX sizes, as Boris S. suggested.
For further points of view on this topic have a look at the Starships & Other Technology forum of the Flare Sci-Fi Forums.